GROMACS version: 2020.4
GROMACS modification: No
I am trying to simulate a diubiquitin chain, where the NZ of a lysine in one ubiquitin (atom 2464) is covalently linked to the C-ter of the other (atom 1962). In the PDB file this ‘isopeptide bond’ is defined at the end by:
CONECT 1962 2464
CONECT 2464 1962
The CONECT lines are eventually ignored when pdb2gmx writes the topology, and apparently when H atoms are added in both molecules somehow the double bonding of C=O at the C-ter breaks down into C-O (x2). So now the “extra oxygen” clashes with NZ, breaking the isopeptide bond I am trying to follow here. Carrying out the simulation this way both of the involved side chains displace both molecules considerably which of course is not what I am looking.
Trying to overcome this I’ve followed a few strategies. At first, and ignoring the appearance of the extra oxygen mentioned above, I applied position restraints at the C-ter and NZ atoms in an attempt to mimic the isopeptide bond as much as possible. After failure I tried to restraint the whole residues (GLY_C-ter and LYS_NZ) but given that they are in separate chains, numbering issues regarding the atoms result in an error message similar to ‘Atom index is out of bounds’ (even when the position restraints were included in the topology file at the right position). Finally, I managed both molecules as a single chain and again tried it with position restraints and even as ‘frozen groups’; although in both cases the atoms remained well fixed, now an artifact is formed between C-ter atom of the 1st ubiquitin and both N-ter and NZ atoms of the second (giving place to this weird ‘pentavalent carbon’).
Is there any other strategy I could try? Or a manner in which I may force this covalent bond to stay? I’m frankly lost.
Thank you very much,